Atomistry » Magnesium » PDB 4s1l-4tny » 4tmz
Atomistry »
  Magnesium »
    PDB 4s1l-4tny »
      4tmz »

Magnesium in PDB 4tmz: Translation Initiation Factor EIF5B (517-858) From C. Thermophilum, Bound to Gtpgammas and Potassium

Protein crystallography data

The structure of Translation Initiation Factor EIF5B (517-858) From C. Thermophilum, Bound to Gtpgammas and Potassium, PDB code: 4tmz was solved by B.Kuhle, F.Ficner, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 47.68 / 2.28
Space group P 41 21 2
Cell size a, b, c (Å), α, β, γ (°) 116.130, 116.130, 120.270, 90.00, 90.00, 90.00
R / Rfree (%) 20 / 23.9

Other elements in 4tmz:

The structure of Translation Initiation Factor EIF5B (517-858) From C. Thermophilum, Bound to Gtpgammas and Potassium also contains other interesting chemical elements:

Potassium (K) 2 atoms
Chlorine (Cl) 2 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Translation Initiation Factor EIF5B (517-858) From C. Thermophilum, Bound to Gtpgammas and Potassium (pdb code 4tmz). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Translation Initiation Factor EIF5B (517-858) From C. Thermophilum, Bound to Gtpgammas and Potassium, PDB code: 4tmz:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 4tmz

Go back to Magnesium Binding Sites List in 4tmz
Magnesium binding site 1 out of 2 in the Translation Initiation Factor EIF5B (517-858) From C. Thermophilum, Bound to Gtpgammas and Potassium


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Translation Initiation Factor EIF5B (517-858) From C. Thermophilum, Bound to Gtpgammas and Potassium within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg902

b:34.7
occ:1.00
O1B B:GSP901 2.0 30.2 1.0
OG1 B:THR537 2.1 30.9 1.0
O B:HOH1013 2.1 35.1 1.0
O3G B:GSP901 2.1 33.8 1.0
O B:HOH1014 2.2 32.9 1.0
OG1 B:THR557 2.2 34.9 1.0
CB B:THR537 3.1 33.3 1.0
CB B:THR557 3.2 35.4 1.0
PB B:GSP901 3.2 33.3 1.0
PG B:GSP901 3.3 36.8 1.0
O3B B:GSP901 3.4 28.9 1.0
N B:THR537 3.9 33.7 1.0
OE2 B:GLU552 4.0 35.6 1.0
CG2 B:THR557 4.1 34.6 1.0
OE1 B:GLU552 4.1 38.8 1.0
CA B:THR537 4.1 36.8 1.0
OD2 B:ASP594 4.2 38.7 1.0
O1A B:GSP901 4.2 32.5 1.0
CG2 B:THR537 4.2 32.3 1.0
O2B B:GSP901 4.2 34.7 1.0
O3A B:GSP901 4.3 42.2 1.0
CA B:THR557 4.3 36.3 1.0
N B:THR557 4.4 38.1 1.0
OD1 B:ASP594 4.4 35.1 1.0
S1G B:GSP901 4.4 33.8 1.0
CD B:GLU552 4.5 36.5 1.0
PA B:GSP901 4.5 38.0 1.0
O2G B:GSP901 4.5 33.6 1.0
O2A B:GSP901 4.5 35.6 1.0
CE B:LYS536 4.6 31.0 1.0
O B:THR595 4.6 31.2 1.0
CG B:ASP594 4.7 36.6 1.0
CB B:LYS536 4.8 31.9 1.0
NZ B:LYS536 5.0 28.2 1.0

Magnesium binding site 2 out of 2 in 4tmz

Go back to Magnesium Binding Sites List in 4tmz
Magnesium binding site 2 out of 2 in the Translation Initiation Factor EIF5B (517-858) From C. Thermophilum, Bound to Gtpgammas and Potassium


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Translation Initiation Factor EIF5B (517-858) From C. Thermophilum, Bound to Gtpgammas and Potassium within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg902

b:48.9
occ:1.00
O3G A:GSP901 2.0 38.9 1.0
OG1 A:THR537 2.0 44.9 1.0
OG1 A:THR557 2.1 37.5 1.0
O2B A:GSP901 2.1 34.9 1.0
O A:HOH1007 2.1 47.7 1.0
O A:HOH1006 2.1 42.6 1.0
CB A:THR557 3.1 38.7 1.0
CB A:THR537 3.1 49.0 1.0
PB A:GSP901 3.3 41.9 1.0
PG A:GSP901 3.3 46.1 1.0
O3B A:GSP901 3.6 40.2 1.0
N A:THR537 3.9 46.6 1.0
CG2 A:THR557 4.0 39.4 1.0
OE1 A:GLU552 4.0 51.6 1.0
OE2 A:GLU552 4.0 48.1 1.0
OD2 A:ASP594 4.0 48.5 1.0
CA A:THR537 4.1 47.8 1.0
CG2 A:THR537 4.2 48.6 1.0
CA A:THR557 4.2 42.2 1.0
O1B A:GSP901 4.3 46.4 1.0
O2A A:GSP901 4.3 47.8 1.0
N A:THR557 4.3 45.7 1.0
OD1 A:ASP594 4.3 48.1 1.0
S1G A:GSP901 4.4 44.4 1.0
CD A:GLU552 4.4 49.1 1.0
O3A A:GSP901 4.5 51.6 1.0
CG A:ASP594 4.5 48.0 1.0
O2G A:GSP901 4.5 40.0 1.0
O A:THR595 4.6 38.4 1.0
CE A:LYS536 4.6 44.3 1.0
PA A:GSP901 4.7 47.3 1.0
O1A A:GSP901 4.7 45.4 1.0
CB A:LYS536 4.8 43.5 1.0

Reference:

B.Kuhle, R.Ficner. A Monovalent Cation Acts As Structural and Catalytic Cofactor in Translational Gtpases. Embo J. 2014.
ISSN: ESSN 1460-2075
PubMed: 25225612
DOI: 10.15252/EMBJ.201488517
Page generated: Mon Dec 14 19:33:36 2020

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy